Sorry to appear negative. I am really happy with Zot6 overall but I must report this issue.

Direct links to pages in PDFs no longer seem to work in Zotero 6. These links take the following form in Zotero 6 vs. :
Zotero6: zotero://open-pdf/library/items/items?page=9&annotation=UFT9HHI4)
Zotero5: zotero://open-pdf/library/items/FQDRHUCLZ?page=9

version => 6.0, platform => MacIntel, oscpu => Intel Mac OS X 10.16, locale => en-GB, appName => Zotero, appVersion => 6.0, extensions => DOI Manager (1.4.2, extension), Zotero LibreOffice Integration (5.0.25.SA.6.0, extension), Zotero Word for Mac Integration (5.0.39.SA.6.0, extension), Mdnotes for Zotero (0.1.3, extension, disabled), Folder Import for Zotero (0.0.2, extension, disabled), Better BibTex for Zotero (6.2.14, extension, disabled)

Congratulations on this excellent release and thank you.

1, Create a new item in Zotero (E.g. add DOI - 10.18637/jss.v059.i10 )
2, Open the PDF
3, Open the Notes pane, next to the PDF, by clicking on the notepad icon in the top-right of the window. This will show two headings 'all notes' and 'item notes'. There will be no notes for this item yet.
4, Add a 'new item note', or 'new item note from annotations' by clicking on the plus sign.
5, In the new note, add a citation to the bottom by clicking on the plus sign at the top of the note pane. The citation will say 'Wickham 2014'.
6, Close the PDF and return to the library where the reference and PDF you created in step 1 is stored. Above the PDF there should be a yellow icon that have (Wickham 2014) written to the right of it.
7, Right-click on the yellow icon and choose 'export note' from the menu that appears.
8, In the dialog box that appears, choose 'markdown' as an export format, and ensure that the 'Include Zotero Links' checkbox is ticked. Click on OK
9, Save the .md file and open it to see what the link looks like.
10, This is what the link looks like in that markdown file: ([Wickham, 2014](zotero://select/library/items/items))

When I do that, I get this:

([Wickham, 2014](zotero://select/library/items/Q5TVQREI))

@martynas_b may have some idea why you'd be getting something different.

No, nothing to do with the system environment, and no reason to test in a VM. If you want to test in something, you can just test in a new Zotero profile.

Can you provide a Debug ID for reproducing this in a new profile?

Oh, it looks like this happens in a non-synced library.

Is that the case in your original library as well?

I am not sure about the original library. It may have been the case. Can I re-install Zotero 5 to see if this is the case? Have to use Zotfile plugin with it to achieve the export AFAIK.

No, it wasn't. I do have a small library up there but not one synced with my current or recent Zotero installations.

How do I get around it? Should I now sync my current library with Zotero.org?

Excellent! Now that I have synced my library it works just fine. I also look forward to the update. Thank you!..

Yaaaay!